1
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Banerjee C, Puchner EM, Kim DH. ULK1 seen at the single-molecule level during autophagy initiation. Autophagy 2024; 20:707-708. [PMID: 37992308 PMCID: PMC10936622 DOI: 10.1080/15548627.2023.2286078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023] Open
Abstract
Macroautophagy/autophagy research often involves overexpressing proteins to investigate their localization, function and activity. However, this approach can disturb the inherent balance of cellular components, potentially affecting the integrity of the autophagy process. With the advent of genome-editing techniques like CRISPR-Cas9, it is now possible to tag endogenous proteins with fluorescent markers, enabling the study of their behaviors under more physiologically relevant conditions. Nevertheless, conventional microscopy methods have limitations in characterizing the behaviors of proteins expressed at endogenous levels. This challenge can be overcome by single-molecule localization microscopy (SMLM) methods, which provide single-molecule sensitivity and super-resolution imaging capabilities. In our recent study, we used SMLM in combination with genome editing to explore the behavior of endogenous ULK1 during autophagy initiation, yielding unprecedented insights into the autophagy initiation process.Abbreviation: ATG13: autophagy related 13; ATG14: autophagy related 14; ATG16L1: autophagy related 16 like 1; BECN1: beclin 1; ER: endoplasmic reticulum; GABARAPL1: GABA type A receptor associated protein like 1; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MTORC1: mechanistic target of rapamycin kinase complex 1; PALM: photo-activated localization microscopy; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15: phosphoinositide-3-kinase regulatory subunit 4; PtdIns3P: phosphatidylinositol-3-phosphate; SMLM: single-molecule localization microscopy; ULK1: unc-51 like autophagy activating kinase 1; WIPI2: WD repeat domain, phosphoinositide interacting 2.
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Affiliation(s)
- Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Twin Cities, USA
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Twin Cities, USA
| | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, USA
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2
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Mehra D, Puchner EM. Correlative Conventional and Super-resolution Photoactivated Localization Microscopy (PALM) Imaging to Characterize Chromatin Structure and Dynamics in Live Mammalian Cells. Bio Protoc 2023; 13:e4850. [PMID: 37900107 PMCID: PMC10603262 DOI: 10.21769/bioprotoc.4850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 10/31/2023] Open
Abstract
A fundamental understanding of gene regulation requires a quantitative characterization of the spatial organization and dynamics of chromatin. The advent of fluorescence super-resolution microscopy techniques such as photoactivated localization microscopy (PALM) presented a breakthrough to visualize structural features with a resolution of ~20 nm in fixed cells. However, until recently the long acquisition time of super-resolution images prevented high-resolution measurements in living cells due to spreading of localizations caused by chromatin motion. Here, we present a step-by step protocol for our recently developed approach for correlatively imaging telomeres with conventional fluorescence and PALM, in order to obtain time-averaged super-resolution images and dynamic parameters in living cells. First, individual single molecule localizations are assigned to a locus as it moves, allowing to discriminate between bound and unbound dCas9 molecules, whose mobilities overlap. By subtracting the telomere trajectory from the localization of bound molecules, the motion blurring is then corrected, and high-resolution structural characterizations can be made. These structural parameters can also be related to local chromatin motion or larger scale domain movement. This protocol therefore improves the ability to analyze the mobility and time-averaged nanoscopic structure of locus-specific chromatin with single-molecule sensitivity.
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Affiliation(s)
- Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Twin Cities, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Twin Cities, MN, USA
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3
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Banerjee C, Mehra D, Song D, Mancebo A, Park JM, Kim DH, Puchner EM. ULK1 forms distinct oligomeric states and nanoscopic structures during autophagy initiation. Sci Adv 2023; 9:eadh4094. [PMID: 37774021 PMCID: PMC10541014 DOI: 10.1126/sciadv.adh4094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Autophagy induction involves extensive molecular and membrane reorganization. Despite substantial progress, the mechanism underlying autophagy initiation remains poorly understood. Here, we used quantitative photoactivated localization microscopy with single-molecule sensitivity to analyze the nanoscopic distribution of endogenous ULK1, the kinase that triggers autophagy. Under amino acid starvation, ULK1 formed large clusters containing up to 161 molecules at the endoplasmic reticulum. Cross-correlation analysis revealed that ULK1 clusters engaging in autophagosome formation require 30 or more molecules. The ULK1 structures with more than the threshold number contained varying levels of Atg13, Atg14, Atg16, LC3B, GEC1, and WIPI2. We found that ULK1 activity is dispensable for the initial clustering of ULK1, but necessary for the subsequent expansion of the clusters, which involves interaction with Atg14, Atg16, and LC3B and relies on Vps34 activity. This quantitative analysis at the single-molecule level has provided unprecedented insights into the behavior of ULK1 during autophagy initiation.
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Affiliation(s)
- Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
- Department of Biomedical Engineering and Physiology, Mayo Clinic, Rochester, MN, USA
| | - Daihyun Song
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Angel Mancebo
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Ji-Man Park
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
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4
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Najt CP, Adhikari S, Heden TD, Cui W, Gansemer ER, Rauckhorst AJ, Markowski TW, Higgins L, Kerr EW, Boyum MD, Alvarez J, Brunko S, Mehra D, Puchner EM, Taylor EB, Mashek DG. Organelle interactions compartmentalize hepatic fatty acid trafficking and metabolism. Cell Rep 2023; 42:112435. [PMID: 37104088 PMCID: PMC10278152 DOI: 10.1016/j.celrep.2023.112435] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/09/2023] [Accepted: 04/10/2023] [Indexed: 04/28/2023] Open
Abstract
Organelle interactions play a significant role in compartmentalizing metabolism and signaling. Lipid droplets (LDs) interact with numerous organelles, including mitochondria, which is largely assumed to facilitate lipid transfer and catabolism. However, quantitative proteomics of hepatic peridroplet mitochondria (PDM) and cytosolic mitochondria (CM) reveals that CM are enriched in proteins comprising various oxidative metabolism pathways, whereas PDM are enriched in proteins involved in lipid anabolism. Isotope tracing and super-resolution imaging confirms that fatty acids (FAs) are selectively trafficked to and oxidized in CM during fasting. In contrast, PDM facilitate FA esterification and LD expansion in nutrient-replete medium. Additionally, mitochondrion-associated membranes (MAM) around PDM and CM differ in their proteomes and ability to support distinct lipid metabolic pathways. We conclude that CM and CM-MAM support lipid catabolic pathways, whereas PDM and PDM-MAM allow hepatocytes to efficiently store excess lipids in LDs to prevent lipotoxicity.
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Affiliation(s)
- Charles P Najt
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Santosh Adhikari
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Timothy D Heden
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Wenqi Cui
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Erica R Gansemer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Adam J Rauckhorst
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Todd W Markowski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Evan W Kerr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Matthew D Boyum
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jonas Alvarez
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Sophia Brunko
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Elias M Puchner
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Eric B Taylor
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA, USA
| | - Douglas G Mashek
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
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5
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Ritz JM, Khakimzhan A, Kim DH, Puchner EM. Characterization of unexpected blue-shifted single molecule fluorescence of JF646 and JF669 for SMLM. Biophys J 2023; 122:279a. [PMID: 36783379 DOI: 10.1016/j.bpj.2022.11.1589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Jacob M Ritz
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Elias M Puchner
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
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6
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Mehra D, Adhikari S, Banerjee C, Puchner EM. Characterizing locus specific chromatin structure and dynamics with correlative conventional and super-resolution imaging in living cells. Nucleic Acids Res 2022; 50:e78. [PMID: 35524554 PMCID: PMC9303368 DOI: 10.1093/nar/gkac314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/08/2022] [Accepted: 05/02/2022] [Indexed: 11/23/2022] Open
Abstract
The dynamic rearrangement of chromatin is critical for gene regulation, but mapping both the spatial organization of chromatin and its dynamics remains a challenge. Many structural conformations are too small to be resolved via conventional fluorescence microscopy and the long acquisition time of super-resolution photoactivated localization microscopy (PALM) precludes the structural characterization of chromatin below the optical diffraction limit in living cells due to chromatin motion. Here we develop a correlative conventional fluorescence and PALM imaging approach to quantitatively map time-averaged chromatin structure and dynamics below the optical diffraction limit in living cells. By assigning localizations to a locus as it moves, we reliably discriminate between bound and unbound dCas9 molecules, whose mobilities overlap. Our approach accounts for changes in DNA mobility and relates local chromatin motion to larger scale domain movement. In our experimental system, we show that compacted telomeres move faster and have a higher density of bound dCas9 molecules, but the relative motion of those molecules is more restricted than in less compacted telomeres. Correlative conventional and PALM imaging therefore improves the ability to analyze the mobility and time-averaged nanoscopic structural features of locus specific chromatin with single molecule sensitivity and yields unprecedented insights across length and time scales.
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Affiliation(s)
- Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Minneapolis MN, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester MN, USA
| | - Santosh Adhikari
- School of Physics and Astronomy, University of Minnesota, Minneapolis MN, USA
| | - Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Minneapolis MN, USA
| | - Elias M Puchner
- School of Physics and Astronomy, University of Minnesota, Minneapolis MN, USA
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7
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Mancebo A, Mehra D, Banerjee C, Kim DH, Puchner EM. Efficient Cross-Correlation Filtering of One- and Two-Color Single Molecule Localization Microscopy Data. Front Bioinform 2021; 1:739769. [PMID: 36303727 PMCID: PMC9581065 DOI: 10.3389/fbinf.2021.739769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/14/2021] [Indexed: 11/25/2022] Open
Abstract
Single molecule localization microscopy has become a prominent technique to quantitatively study biological processes below the optical diffraction limit. By fitting the intensity profile of single sparsely activated fluorophores, which are often attached to a specific biomolecule within a cell, the locations of all imaged fluorophores are obtained with ∼20 nm resolution in the form of a coordinate table. While rendered super-resolution images reveal structural features of intracellular structures below the optical diffraction limit, the ability to further analyze the molecular coordinates presents opportunities to gain additional quantitative insights into the spatial distribution of a biomolecule of interest. For instance, pair-correlation or radial distribution functions are employed as a measure of clustering, and cross-correlation analysis reveals the colocalization of two biomolecules in two-color SMLM data. Here, we present an efficient filtering method for SMLM data sets based on pair- or cross-correlation to isolate localizations that are clustered or appear in proximity to a second set of localizations in two-color SMLM data. In this way, clustered or colocalized localizations can be separately rendered and analyzed to compare other molecular properties to the remaining localizations, such as their oligomeric state or mobility in live cell experiments. Current matrix-based cross-correlation analyses of large data sets quickly reach the limitations of computer memory due to the space complexity of constructing the distance matrices. Our approach leverages k-dimensional trees to efficiently perform range searches, which dramatically reduces memory needs and the time for the analysis. We demonstrate the versatile applications of this method with simulated data sets as well as examples of two-color SMLM data. The provided MATLAB code and its description can be integrated into existing localization analysis packages and provides a useful resource to analyze SMLM data with new detail.
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Affiliation(s)
- Angel Mancebo
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
| | - Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
| | - Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
| | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Elias M. Puchner,
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8
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Adhikari S, Moscatelli J, Puchner EM. Quantitative live-cell PALM reveals nanoscopic Faa4 redistributions and dynamics on lipid droplets during metabolic transitions of yeast. Mol Biol Cell 2021; 32:1565-1578. [PMID: 34161133 PMCID: PMC8351750 DOI: 10.1091/mbc.e20-11-0695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Lipid droplets (LDs) are dynamic organelles for lipid storage and homeostasis. Cells respond to metabolic changes by regulating the spatial distribution of LDs and enzymes required for LD growth and turnover. The small size of LDs precludes the observation of their associated enzyme densities and dynamics with conventional fluorescence microscopy. Here we employ quantitative photo-activated localization microscopy to study the density of the fatty acid (FA) activating enzyme Faa4 on LDs in live yeast cells with single-molecule sensitivity and 30 nm resolution. During the log phase LDs colocalize with the endoplasmic reticulum (ER) where their emergence and expansion are mediated by the highest observed Faa4 densities. During transition to the stationary phase, LDs with a ∼2-fold increased surface area translocate to the vacuolar surface and lumen and exhibit a ∼2.5-fold increase in Faa4 density. The increased Faa4 density on LDs further suggests its role in LD expansion, is caused by its ∼5-fold increased expression level, and is specific to exogenous FA chain-lengths. When lipolysis is induced by refreshed medium, Faa4 shuttles through ER- and lipophagy to the vacuole, where it may activate FAs for membrane expansion and degrade Faa4 to reset its cellular abundance to levels in the log phase.
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Affiliation(s)
- Santosh Adhikari
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Physics and Nanotechnology (PAN), Minneapolis, MN 55455
| | - Joe Moscatelli
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Physics and Nanotechnology (PAN), Minneapolis, MN 55455
| | - Elias M Puchner
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Physics and Nanotechnology (PAN), Minneapolis, MN 55455
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9
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Adhikari S, Moscatelli J, Puchner EM. Quantitative Live-Cell Palm Reveals Nanoscopic Faa4 Redistributions and Dynamics on Lipid Droplets during Metabolic Transitions in Yeast. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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10
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Mehra D, Banerjee C, Adhikari S, Ritz JM, Mancebo A, Puchner EM. Characterization of Locus Specific Chromatin Structure and Dynamics using Correlative Conventional Super Resolution Crispr dCas9/Ms2 Imaging. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Mancebo A, Ritz JM, Puchner EM. Development of Diffusion Contrast Photo-Activated Localization Microscopy to Detect Sparse Protein Interactions at High Background. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.2203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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12
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Adhikari S, Banerjee C, Moscatelli J, Puchner EM. Conventional BODIPY Conjugates for Live-Cell Super-Resolution Microscopy and Single-Molecule Tracking. J Vis Exp 2020. [PMID: 32568221 DOI: 10.3791/60950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Single molecule localization microscopy (SMLM) techniques overcome the optical diffraction limit of conventional fluorescence microscopy and can resolve intracellular structures and the dynamics of biomolecules with ~20 nm precision. A prerequisite for SMLM are fluorophores that transition from a dark to a fluorescent state in order to avoid spatio-temporal overlap of their point spread functions in each of the thousands of data acquisition frames. BODIPYs are well-established dyes with numerous conjugates used in conventional microscopy. The transient formation of red-shifted BODIPY ground-state dimers (DII) results in bright single molecule emission enabling single molecule localization microscopy (SMLM). Here we present a simple but versatile protocol for SMLM with conventional BODIPY conjugates in living yeast and mammalian cells. This procedure can be used to acquire super-resolution images and to track single BODIPY-DII states to extract spatio-temporal information of BODIPY conjugates. We apply this procedure to resolve lipid droplets (LDs), fatty acids, and lysosomes in living yeast and mammalian cells at the nanoscopic length scale. Furthermore, we demonstrate the multi-color imaging capability with BODIPY dyes when used in conjunction with other fluorescent probes. Our representative results show the differential spatial distribution and mobility of BODIPY-fatty acids and neutral lipids in yeast under fed and fasted conditions. This optimized protocol for SMLM can be used with hundreds of commercially available BODIPY conjugates and is a useful resource to study biological processes at the nanoscale far beyond the applications of this work.
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Affiliation(s)
- Santosh Adhikari
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Physics and Nanotechnology (PAN)
| | - Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Physics and Nanotechnology (PAN)
| | - Joe Moscatelli
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Physics and Nanotechnology (PAN); Middlebury College
| | - Elias M Puchner
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Physics and Nanotechnology (PAN);
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Mancebo A, DeMars L, Ertsgaard CT, Puchner EM. Precisely calibrated and spatially informed illumination for conventional fluorescence and improved PALM imaging applications. Methods Appl Fluoresc 2020; 8:025004. [PMID: 31995796 DOI: 10.1088/2050-6120/ab716a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Spatial light modulation using cost efficient digital micromirror devices (DMD) is finding broad applications in fluorescence microscopy due to the reduction of phototoxicity and bleaching and the ability to manipulate proteins in optogenetic experiments. However, precise illumination by DMDs and their application to single-molecule localization microscopy (SMLM) remained a challenge because of non-linear distortions between the DMD and camera coordinate systems caused by optical components in the excitation and emission path. Here we develop a fast and easy to implement calibration procedure that determines these distortions and matches the DMD and camera coordinate system with a precision below the optical diffraction limit. As a result, a region from a fluorescence image can be selected with a higher precision for illumination compared to a rigid transformation allowed by manual alignment of the DMD. We first demonstrate the application of our precisely calibrated light modulation by performing a proof of concept fluorescence recovery after photobleaching experiment with the endoplasmic reticulum-localized protein IRE1 fused to GFP in budding yeast (S. cerevisiae). Next, we develop a spatially informed photoactivation approach for SMLM in which only regions of the cell that contain photoactivatable fluorescent proteins are selected for photoactivation. The reduced exposure of the cells to 405 nm light increased the possible imaging time by 44% until phototoxic effects cause a dominant fluorescence background and a change in cell morphology. As a result, the mean number of reliable single-molecule localizations was also significantly increased by 28%. Since the localization precision and the ability for single-molecule tracking is not altered compared to traditional photoactivation of the entire field of view, spatially informed photoactivation significantly improves the quality of SMLM images and single-molecule tracking data. Our precise calibration method therefore lays the foundation for improved SMLM with active feedback photoactivation far beyond the applications in this work.
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Affiliation(s)
- Angel Mancebo
- School of Physics and Astronomy, University of Minnesota, Physics and Nanotechnology, 115 Union St. SE, Minneapolis, MN 55455, United States of America
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14
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Banerjee C, Song D, Kim DH, Puchner EM. Quantitative Superresolution Microscopy Reveals the Critical Role of ULK1 Oligomeric States and Sub-Cellular Localization in Phagophore Maturation. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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15
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Mehra D, Banerjee C, Adhikari S, Clark KJ, Ekker SC, Puchner EM. Characterization of dCas9 Interaction Kinetics and Local Chromatin Structure in Live Human Cells using Palm Superresolution Microscopy. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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16
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Mancebo A, Puchner EM. Mitigating Phototoxicity in Single-Molecule Localization Microscopy Using Precisely Calibrated and Spatially Informed Photoactivation. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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17
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Adhikari S, Moscatelli J, Puchner EM. Live-Cell Superresolution Microscopy of Faa4 Re-Distribution on Lipid Droplets during Metabolic Transitions in Yeast. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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18
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Abstract
We develop and employ the Fluorescence-Activating and absorption-Shifting Tag (FAST) system for super-resolution (SR) imaging and single-molecule tracking based on single-molecule localizations. The fast off rate of fluorogen binding, combined with its spatially well-separated labeling of the densely expressed FAST fusion proteins, allowed single-molecule measurements to be performed in both living and fixed cells. The well-separated fluorescence localization density was achieved by either reversibly controlling the fluorogen concentration or by irreversibly photobleaching the FAST-fluorogen complex. The experimentally determined resolution of 28 nm allowed us to resolve Ensconsin-labeled microtubules and to track single molecules in mitochondria. Our results demonstrate that FAST is well-suited for single-molecule localization microscopy (SMLM). The small size and the availability of spectrally distinct fluorogens present unique advantages of the FAST system as a potential orthogonal labeling strategy that could be applied in conjunction with existing super-resolution dyes and photoactivatable proteins in versatile imaging applications.
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Affiliation(s)
- Elizabeth M. Smith
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455
| | - Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455
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19
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Smith EM, Gautier A, Puchner EM. Development and Optimization of the Y-Fast:Fluorogen System for Super-Resolution Imaging. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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20
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Puchner EM, Adhikari S. Quantitative and Motion-Corrected Super-Resolution Imaging of Endosome Dynamics in Living Cells. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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21
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Ramírez MP, Rivera M, Quiroga-Roger D, Bustamante A, Vega M, Baez M, Puchner EM, Wilson CAM. Single molecule force spectroscopy reveals the effect of BiP chaperone on protein folding. Protein Sci 2017; 26:1404-1412. [PMID: 28176394 DOI: 10.1002/pro.3137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/18/2017] [Accepted: 02/03/2017] [Indexed: 11/10/2022]
Abstract
BiP (Immunoglobulin Binding Protein) is a member of the Hsp70 chaperones that participates in protein folding in the endoplasmic reticulum. The function of BiP relies on cycles of ATP hydrolysis driving the binding and release of its substrate proteins. It still remains unknown how BiP affects the protein folding pathway and there has been no direct demonstration showing which folding state of the substrate protein is bound by BiP, as previous work has used only peptides. Here, we employ optical tweezers for single molecule force spectroscopy experiments to investigate how BiP affects the folding mechanism of a complete protein and how this effect depends on nucleotides. Using the protein MJ0366 as the substrate for BiP, we performed pulling and relaxing cycles at constant velocity to unfold and refold the substrate. In the absence of BiP, MJ0366 unfolded and refolded in every cycle. However, when BiP was added, the frequency of folding events of MJ0366 significantly decreased, and the loss of folding always occurred after a successful unfolding event. This process was dependent on ATP and ADP, since when either ATP was decreased or ADP was added, the duration of periods without folding events increased. Our results show that the affinity of BiP for the substrate protein increased in these conditions, which correlates with previous studies in bulk. Therefore, we conclude that BiP binds to the unfolded state of MJ0366 and prevents its refolding, and that this effect is dependent on both the type and concentration of nucleotides.
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Affiliation(s)
- María Paz Ramírez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile.,Laboratory of Cellular and Molecular Biophysics, School of Physics & Astronomy, University of Minnesota, Twin Cities, Minnesota
| | - Maira Rivera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Diego Quiroga-Roger
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Andrés Bustamante
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Marcela Vega
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Elias M Puchner
- Laboratory of Cellular and Molecular Biophysics, School of Physics & Astronomy, University of Minnesota, Twin Cities, Minnesota
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
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22
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Sydor AM, Czymmek KJ, Puchner EM, Mennella V. Super-Resolution Microscopy: From Single Molecules to Supramolecular Assemblies. Trends Cell Biol 2015; 25:730-748. [DOI: 10.1016/j.tcb.2015.10.004] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/03/2015] [Accepted: 10/05/2015] [Indexed: 11/25/2022]
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23
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Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA. Remote control of therapeutic T cells through a small molecule-gated chimeric receptor. Science 2015; 350:aab4077. [PMID: 26405231 DOI: 10.1126/science.aab4077] [Citation(s) in RCA: 494] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/09/2015] [Indexed: 12/17/2022]
Abstract
There is growing interest in using engineered cells as therapeutic agents. For example, synthetic chimeric antigen receptors (CARs) can redirect T cells to recognize and eliminate tumor cells expressing specific antigens. Despite promising clinical results, these engineered T cells can exhibit excessive activity that is difficult to control and can cause severe toxicity. We designed "ON-switch" CARs that enable small-molecule control over T cell therapeutic functions while still retaining antigen specificity. In these split receptors, antigen-binding and intracellular signaling components assemble only in the presence of a heterodimerizing small molecule. This titratable pharmacologic regulation could allow physicians to precisely control the timing, location, and dosage of T cell activity, thereby mitigating toxicity. This work illustrates the potential of combining cellular engineering with orthogonal chemical tools to yield safer therapeutic cells that tightly integrate cell-autonomous recognition and user control.
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Affiliation(s)
- Chia-Yung Wu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA
| | - Kole T Roybal
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA
| | - Elias M Puchner
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - James Onuffer
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA.
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. The Cell Propulsion Lab, an NIH Nanomedicine Development Center, University of California, San Francisco, CA 94158, USA. Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA.
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24
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Affiliation(s)
- Elias M Puchner
- University of California San Francisco, Department of Cellular & Molecular Pharmacology, Genentech Hall Room N414, 600 - 16th Street, San Francisco, CA 94158, USA.
| | - Bo Huang
- Department of Pharmaceutical Chemistry, Department of Biochemistry and Biophysics, University of California, San Francisco, Byers Hall Room 303A, 1700 4th St, MC 2532, San Francisco, CA 94158, USA.
| | - Hermann E Gaub
- Center for Nanoscience and Department of Physics, University of Munich, Amalienstraße 54, 80799 Munich, Germany.
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25
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Puchner EM, Walter JM, Kasper R, Huang B, Lim WA. Probing Molecular Number Variability in Intracellular Structures using Photoswitchable Fluorescent Proteins. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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26
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Affiliation(s)
- Elias M. Puchner
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158;
| | - Hermann E. Gaub
- Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany;
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27
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Strackharn M, Stahl SW, Puchner EM, Gaub HE. Functional assembly of aptamer binding sites by single-molecule cut-and-paste. Nano Lett 2012; 12:2425-2428. [PMID: 22468898 DOI: 10.1021/nl300422y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Bottom up assembly of functional molecular ensembles with novel properties emerging from composition and arrangement of its constituents is a prime goal of nanotechnology. By single-molecule cut-and-paste we assembled binding sites for malachite green in a molecule-by-molecule assembly process from the two halves of a split aptamer. We show that only a perfectly joined binding site immobilizes the fluorophore and enhances the fluorescence quantum yield by several orders of magnitude. To corroborate the robustness of this approach we produced a micrometer-sized structure consisting of more than 500 reconstituted binding sites. To the best of our knowledge, this is the first demonstration of one by one bottom up functional biomolecular assembly.
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Affiliation(s)
- Mathias Strackharn
- Center for Nanoscience and Department of Physics, University of Munich, Amalienstrasse 54, 80799 Munich, Germany
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28
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Stahl SW, Puchner EM, Alexandrovich A, Gautel M, Gaub HE. A conditional gating mechanism assures the integrity of the molecular force-sensor titin kinase. Biophys J 2012; 101:1978-86. [PMID: 22004752 DOI: 10.1016/j.bpj.2011.09.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/11/2011] [Accepted: 09/06/2011] [Indexed: 12/16/2022] Open
Abstract
As more and more recent investigations point out, force plays an important role in cellular regulation mechanisms. Biological responses to mechanical stress are often based on force-induced conformational changes of single molecules. The force sensor, titin kinase, is involved in a signaling complex that regulates protein turnover and transcriptional adaptation in striated muscle. The structural architecture of such a force sensor determines its response to force and must assure both activity and mechanical integrity, which are prerequisites for its function. Here, we use single-molecule force-clamp spectroscopy to show that titin kinase is organized in such a way that the regulatory domains have to unfold before secondary structure elements that determine the overall fold and catalytic function. The stepwise unfolding over many barriers with a topologically determined sequence assures that the protein can react to force by conformational changes while maintaining its structural integrity.
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Affiliation(s)
- Stefan W Stahl
- Center for NanoScience, Ludwig-Maximilians-University Munich, Munich, Germany
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29
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Heus HA, Puchner EM, van Vugt-Jonker AJ, Zimmermann JL, Gaub HE. Atomic force microscope-based single-molecule force spectroscopy of RNA unfolding. Anal Biochem 2011; 414:1-6. [DOI: 10.1016/j.ab.2011.03.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 01/28/2023]
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30
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Affiliation(s)
- Michael Geisler
- IMETUM, Physics Department, CeNS and CIPSM, Technische Universität München, 85748 Garching, Germany, Key Laboratory for Computational Biology, MPG-CAS Partner Institute for Computational Biology, Chinese Academy of Sciences, 200031 Shanghai, China, Bioquant, Heidelberg University, 69120 Heidelberg, Germany, and Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany
| | - Senbo Xiao
- IMETUM, Physics Department, CeNS and CIPSM, Technische Universität München, 85748 Garching, Germany, Key Laboratory for Computational Biology, MPG-CAS Partner Institute for Computational Biology, Chinese Academy of Sciences, 200031 Shanghai, China, Bioquant, Heidelberg University, 69120 Heidelberg, Germany, and Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany
| | - Elias M. Puchner
- IMETUM, Physics Department, CeNS and CIPSM, Technische Universität München, 85748 Garching, Germany, Key Laboratory for Computational Biology, MPG-CAS Partner Institute for Computational Biology, Chinese Academy of Sciences, 200031 Shanghai, China, Bioquant, Heidelberg University, 69120 Heidelberg, Germany, and Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany
| | - Frauke Gräter
- IMETUM, Physics Department, CeNS and CIPSM, Technische Universität München, 85748 Garching, Germany, Key Laboratory for Computational Biology, MPG-CAS Partner Institute for Computational Biology, Chinese Academy of Sciences, 200031 Shanghai, China, Bioquant, Heidelberg University, 69120 Heidelberg, Germany, and Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany
| | - Thorsten Hugel
- IMETUM, Physics Department, CeNS and CIPSM, Technische Universität München, 85748 Garching, Germany, Key Laboratory for Computational Biology, MPG-CAS Partner Institute for Computational Biology, Chinese Academy of Sciences, 200031 Shanghai, China, Bioquant, Heidelberg University, 69120 Heidelberg, Germany, and Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany
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31
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Puchner EM, Gaub HE. Exploring the conformation-regulated function of titin kinase by mechanical pump and probe experiments with single molecules. Angew Chem Int Ed Engl 2010; 49:1147-50. [PMID: 20077447 DOI: 10.1002/anie.200905956] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Elias M Puchner
- Lehrstuhl für Angewandte Physik, Center for Nanoscience and Center for Integrated Protein Science Munich, Ludwig-Maximilians Universität München, Amalienstrasse 54, 80799 München, Germany
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32
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Cordes T, Strackharn M, Stahl SW, Summerer W, Steinhauer C, Forthmann C, Puchner EM, Vogelsang J, Gaub HE, Tinnefeld P. Resolving single-molecule assembled patterns with superresolution blink-microscopy. Nano Lett 2010; 10:645-651. [PMID: 20017533 DOI: 10.1021/nl903730r] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In this paper we experimentally combine a recently developed AFM-based molecule-by-molecule assembly (single-molecule cut-and-paste, SMCP) with subdiffraction resolution fluorescence imaging. Using "Blink-Microscopy", which exploits the fluctuating emission of single molecules for the reconstruction of superresolution images, we resolved SMCP assembled structures with features below the diffraction limit. Artificial line patterns then served as calibration structures to characterize parameters, such as the labeling density, that can influence resolution of Blink-Microscopy besides the localization precision of a single molecule. Finally, we experimentally utilized the adjustability of blink parameters to demonstrate the general connection of photophysical parameters with spatial resolution and acquisition time in superresolution microscopy.
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Affiliation(s)
- Thorben Cordes
- Applied Physics-Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität, Amalienstrasse 54, D-80799 München, Germany
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33
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Puchner EM, Gaub HE. Force and function: probing proteins with AFM-based force spectroscopy. Curr Opin Struct Biol 2009; 19:605-14. [DOI: 10.1016/j.sbi.2009.09.005] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 08/28/2009] [Accepted: 09/17/2009] [Indexed: 10/20/2022]
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Abstract
Integrating single molecule force spectroscopy with fluorescence-based techniques allows the manipulation of an enzyme with a periodic stretching and relaxation protocol while simultaneously monitoring its catalytic activity. After releasing the stretching force we observe a higher probability for enzymatic activity at a time of 1.7 s. A detailed theoretical analysis reveals that the relaxation from the force-induced enzyme conformation to the observed active conformation follows a cascade reaction with several steps and a free energy difference of at least 8 k(B)T. Our study clearly points out the direct influence of force on enzymatic activity and opens up a new way to study and manipulate (bio)catalytic reactions at the single molecule level.
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Affiliation(s)
- Hermann Gumpp
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Center for Integrated Protein Science Munich, LMU München, D-80799 München, Germany
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35
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Abstract
Photothermal cantilever excitation provides a fast and easy to implement means to control the deflection of standard atomic force microscopy cantilevers. Minute heat pulses yield deflections on the order of several tens of nanometers or when the deflection is kept constant, forces of several hundreds of piconewton can be applied. In our case these pulses resulted in less than 1 K temperature changes at the sample position. Here we present and characterize the implementation of photothermal actuation for single-molecule force-spectroscopy experiments. When molecules are stretched under force-clamp conditions, fast control cycles that re-establish the pulling force after the rupture of molecular domains are essential for detecting the complete unfolding pattern with high precision. By combining the fast response of photothermal cantilever excitation with a conventional piezoactuator, a fast force-clamp with high accuracy and large working distances is reached. Simple feedback mechanisms and standard cantilever geometries lead to step response times of less than 90 micros, which is more than one order of magnitude faster than those of conventional force-clamp systems that are based only on piezo feedback. We demonstrate the fast and accurate performance of the setup by unfolding a protein construct consisting of one green fluorescent protein and eight surrounding immunoglobulin domains at constant force.
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Affiliation(s)
- Stefan W Stahl
- Chair for Applied Physics and Center for NanoScience, Ludwig-Maximilians-University, Amalienstr. 54, Munich D-80799, Germany.
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36
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Gumpp H, Stahl SW, Strackharn M, Puchner EM, Gaub HE. Ultrastable combined atomic force and total internal reflection fluorescence microscope [corrected]. Rev Sci Instrum 2009; 80:063704. [PMID: 19566207 DOI: 10.1063/1.3148224] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Combining atomic force microscope (AFM) with other microscopy techniques has expanded the range of potential applications for single molecule investigations dramatically. Particularly hybrid instruments with total internal reflection fluorescence (TIRF) excitation have opened new routes in life sciences. Here we present a novel design for such a hybrid microscope, which overcomes the limitations of conventional combinations caused by their limited mechanical stability. A thorough analysis of the noise spectra and a comparison of the different designs and the different operation modes are given. With this instrument we demonstrate single molecule manipulation by AFM and simultaneous TIRF imaging.
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Affiliation(s)
- H Gumpp
- Chair for Applied Physics and Center for NanoScience, Ludwig-Maximilians-University Munich, Amalienstr. 54, D-80799 Munich, Germany
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37
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Puchner EM, Alexandrovich A, Kho AL, Hensen U, Schäfer LV, Brandmeier B, Gräter F, Grubmüller H, Gautel M, Gaub HE. Single-Molecule Force Spectroscopy Reveals the Function of Titin Kinase as Force Sensor. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.3401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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38
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Kufer SK, Strackharn M, Stahl SW, Gumpp H, Puchner EM, Gaub HE. Optically monitoring the mechanical assembly of single molecules. Nat Nanotechnol 2009; 4:45-49. [PMID: 19119282 DOI: 10.1038/nnano.2008.333] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 10/22/2008] [Indexed: 05/27/2023]
Abstract
Bottom-up assembly at the level of individual molecules requires a combination of utmost spatial precision and efficient monitoring. We have previously shown how to 'cut-and-paste' single molecules, and other groups have demonstrated that it is possible to beat the diffraction limit in optical microscopy. Here we show that a combination of single-molecule cut-and-paste surface assembly, total internal reflection fluorescence microscopy and atomic force microscopy can be used to deposit individual fluorophores in well-defined nanoscale patterns and also to monitor the process in real time with nanometre precision. Although the size of the pattern is well below the optical resolution of the microscope, the individual dyes are identified by localizing the centroids and detecting the photobleaching of the fluorophores. With this combination of methods, individual dyes or labelled biomolecules can be arranged at will for specific functions, such as coupled fluorophore systems or tailored enzyme cascades, and monitored with nanoscale precision.
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39
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Puchner EM, Kufer SK, Strackharn M, Stahl SW, Gaub HE. Nanoparticle self-assembly on a DNA-scaffold written by single-molecule cut-and-paste. Nano Lett 2008; 8:3692-3695. [PMID: 18826290 DOI: 10.1021/nl8018627] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Self-assembly guided by molecular recognition has in the past been employed to assemble nanoparticle superstructures like hypercrystals or nanoparticle molecules. An alternative approach, the direct molecule-by-molecule assembly of nanoscale superstructures, was demonstrated recently. Here we present a hybrid approach where we first assemble a pattern of binding sites one-by-one at a surface and then allow different nanoparticles to attach by self-assembly. For this approach, biotin bearing DNA oligomers were picked up from a depot using a cDNA strand bound to an AFM tip. These units were deposited in the target area by hybridization, forming a recognition pattern on this surface. Fluorescent semiconductor nanoparticles conjugated with streptavidin were allowed to assemble on this scaffold and to form the final nanoparticle superstructures.
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Affiliation(s)
- Elias M Puchner
- Chair for Applied Physics, Ludwig-Maximilians-Universität Munich, Amalienstrasse 54, 80799 Munich
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40
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Morfill J, Neumann J, Blank K, Steinbach U, Puchner EM, Gottschalk KE, Gaub HE. Force-based Analysis of Multidimensional Energy Landscapes: Application of Dynamic Force Spectroscopy and Steered Molecular Dynamics Simulations to an Antibody Fragment–Peptide Complex. J Mol Biol 2008; 381:1253-66. [DOI: 10.1016/j.jmb.2008.06.065] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 06/18/2008] [Accepted: 06/20/2008] [Indexed: 11/25/2022]
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41
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Abstract
We introduce a method for the bottom-up assembly of biomolecular structures that combines the precision of the atomic force microscope (AFM) with the selectivity of DNA hybridization. Functional units coupled to DNA oligomers were picked up from a depot area by means of a complementary DNA strand bound to an AFM tip. These units were transferred to and deposited on a target area to create basic geometrical structures, assembled from units with different functions. Each of these cut-and-paste events was characterized by single-molecule force spectroscopy and single-molecule fluorescence microscopy. Transport and deposition of more than 5000 units were achieved, with less than 10% loss in transfer efficiency.
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Affiliation(s)
- S K Kufer
- Center for Nanoscience and Department of Physics, University of Munich, Amalienstrasse 54, 80799 Munich, Germany
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